


Molly Hooper: Agent of S.H.I.E.L.D.

by geishakamameha



Category: Agents of S.H.I.E.L.D. (TV), Marvel Cinematic Universe, Sherlock (TV), The Avengers (Marvel Movies)
Genre: Alternate Universe - Canon Divergence, Crossover, Gen
Language: English
Status: In-Progress
Published: 2014-07-06
Updated: 2014-07-25
Packaged: 2018-02-07 15:38:22
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings, No Archive Warnings Apply
Chapters: 4
Words: 4,709
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/1904466
Author URL: https://archiveofourown.org/users/geishakamameha/pseuds/geishakamameha
Summary: <blockquote class="userstuff">
              <p>Molly Hooper is thrown in for a loop when she's been plucked out of the Hub to spy on Sherlock Holmes to assess his potential to be a SHIELD recruit.</p>
            </blockquote>





	1. Chapter 1

**Author's Note:**

> This is my first work here. Most of my works are crossovers and are on FF.net. I haven't dropped any of those but I usually lose interest and inspiration. 
> 
> I have an outline this time so I know where I'm going. So I hope to finish this and the outline is pretty long so it might potentially be a series.
> 
> I posted this on my tumblr but since I've got no followers yet, I haven't gotten feedback. I have started chapter 3 and I'm 2 pages in. 
> 
> Be kind but I'd like constructive critiques. And the links to my tumblr account and FF.net account are in my profile :D

She crosses her legs as she leans on the corner of the diner booth. Her fingers were playing with the edges of the manila folder on the table. The waitress puts down the cup and saucer and pours the steaming brown liquid. The sugar and cream follows after. The woman in the booth uncrosses her legs to fix her coffee the way she liked it. Her peripheral had caught sight of the man in the leather trench coat. He jogs a bit as the rain outside started to pour. The diner bell rings as the dark man with the heavy coat enters and looks around before spotting the woman in the corner of the diner. He shrugs his coat to shake off the water and swiftly walks toward the woman. She wasn’t hard to spot. Her red locks would always standout anywhere. He slides on the opposite seat across from her and she slides the folder to him.

“That didn’t take too long, didn’t it?” Nick Fury starts as he opens the report.

“I don’t see how this man could be SHIELD material. He’s not even the same level as Stark.” Natasha Romanov takes a sip of her coffee with one hand as the other drums its fingers on the table.  Fury doesn’t look up as he kept reading the file.

“He’s an exceptional person. I’ve seen him in action with Scotland Yard with that Daniels case, “ Natasha was about to cut him off but Fury continues, “But yeah, he doesn’t play well with others like your last recommendation.

 “His brain works 10 times faster than the normal person can but he can’t be motivated to work for us.” She rests head against her perched arm on the window pane with her eyes staring at the droplets on the glass.

“Says here he likes puzzles. That’s a way in.” Fury puts down the file and rests is right hand on the table.

“Yeah… But that just means we need to be always a few steps ahead. I don’t have that time and patience.”

“I take it that he’s not the kind of man that you can persuade with your assets either…” Fury smirks as he leans forward to rest his head on his clasped hands where his elbows are rests on the table.

“Oh god no!” She exclaims. She combs back her hair with her right hand.

This assignment had her in England for a week to follow and scout for the one and only consulting detective as a possible recruit. Fury had flagged him after his visit to London a few months back. He saw potential and had his best agent to look into it. Natasha was intrigued at first but after a week of seeing this Sherlock Holmes from a vantage point, she concluded that a direct approach from her was not the best course of action. In her honest opinion, Fury was wasting his time. Holmes is a loose cannon and he would bypass most of the SHIELD training with his annoying wit and powers of deduction. He might possible scare away other personnel in the process. The man was not worth the trouble. 

But if Fury would insist, she put an alternative recommendation at the end of the report.

“Then we’ll get someone else. But I think she’s overqualified for this, Romanov. It’s also not her skill strength. She only goes undercover for short missions. “ Fury takes a beat waiting for her to expound more on the alternative recommendation.

“I know. But I have a plan,” Natasha meets his eye with a smirk. He only raises his brow and mirrors her knowing smile.

“Then I can trust you to handle her training.” He slides off the bench and stands up, signaling the end of their meeting.

Natasha looks up and slightly nods. “I’ll leave for the Hub in a few hours. But clear it with Hand. She hates surprises.”

Fury rolls his eyes and proceeds to leave. Natasha’s eyes follow his back as he heads back out in the rain. Right on time, a black SUV arrives in front of the diner. She grabs the folder and tucks it under her jacket. She waits out the rain before heading out to the airstrip.

She takes out her phone as she walks to her ride parked a few blocks away.

It takes a few rings before the other person picks up.

“Hello? Natasha?” a voice with a proper English accent calls from the other line.

“Hey there Dr. Hooper,” Natasha coyly uses her proper title.

“I thought you were in England. Are you still there now? I haven’t been back there in ages. Do you have time to see the sights? “ Dr. Hooper loads all her questions to Natasha and the redhead only chuckles in amusement.

“I was but I’m back in New York so no, I’m not there anymore. I didn’t see much but I’m sure you’ll get the opportunity to go back soon and see some sights yourself. Listen, I’ll be in the Hub in a few hours. I’ll fill you in with the details then.”

“What?” The person on the other line exclaims. “What does that—“ Natasha smirks as she hangs up the phone. She gets in her car and drives to the airstrip where a quintjet was waiting to take her to the Hub. 


	2. Chapter 2

“Okay, run this by me again?” Molly Hooper shakes her head in disbelief and denial. She tries to appear busy fiddling with the test tubes and flasks on the lab desk in front of her. She didn’t want to directly look at Natasha who was tilting her head in amusement at her discomfort.

Natasha presses her palms on the table as she leans in. “London, undercover, Sherlock Holmes… I’ll give you time to process.” She smirks as Molly furrows her brows in with a glare that was intended to look intimidating except she just looked like a kid who didn’t get her way.

“But isn’t this more your wheelhouse? You just did it with Tony Stark some time ago…” Molly stops fidgeting and slumps on the rotating stool near Natasha.

“You know, I wouldn’t recommend you to do this if you aren’t qualified.” Natasha takes the other stool and slides it beside Molly’s. “Besides, this will be very different from your usual assignments.” She takes the folder containing the brief and slides it to Molly. The doctor places her hand tentatively over it and painstakingly opens it. She wants to drag it out so she shuts her eyes tightly and releases the breath she didn’t know she was holding.

The first thing she reads is the undercover alias. Her head zooms to look at Natasha’s face and gives her a horrified look. “Is this a fuckin’ joke, Romanov?” She takes the first page of the brief as the rest of the folder falls to the floor, scattering all over. She holds the page, crumpling the top with her tightly clenched fist.

“Nop-puh,” the redhead pops the p. She tilts her head, trying to act cute and smiles.

“Molly Hooper is not an alias! That is my real name!” Molly starts pacing. “I’m not going back to London as myself! This is has to be against SHIELD protocol…” Her frantic mind is recalling scenarios of her childhood in England. She was a loner and a pariah because of her intellect and was always ignored or bullied by her peers. It was hard fitting in anywhere since she was too smart to be with kids her own age and being advanced 3 years in her secondary schooling had her picked on by the older kids. Her relief came when she entered university at 15 but only to lose her father after graduating 3 years later. After finishing medical school at 22, she gets recruited by SHIELD as part of a medical research team. Her first assignments were in the Fridge, studying the different people who have come in contact with radiation. Sometimes she was sent on field to retrieve and contain these people. After her almost fatal encounter with a hostile subject, she was transferred to DC in the Triskelion. She was put more on field to hone her skills in order to avoid future incidents when encountering aggressive enemies. After 5 years of fieldwork, she requests a transfer to a quiet lab space in the Hub, deciding that she wanted to do more research and publish papers as Dr. Molly Hooper. Most of her papers were of the forensic type. She left out the details about her encounters as a SHIELD agent but most of her data came from her time in the field.

Molly was finally in a relatively calm and quiet place in her SHIELD career. Natasha was putting her back out there with this mission. And to top it off, she had to be herself. After several minutes of pacing, she turns to Natasha who was able to save the papers from being trampled on by her frantic feet. The spy holds out the folder in her hand, waiting for Molly to calm down.

“Read the brief before you go ballistic, okay?” The doctor narrows her eyes at her and snatches the folder from her hand.

She skims the file only to read a highly detailed backstory that was nearly identical to her own, a profile of her undercover personality, and even a list of her appearance that needed to change. She huffs a bit after reading the part of ‘being a pushover by being very accommodating to her workmates’.  She licks her lips and bites it after glaring at Natasha some more. “This…” she says holding up the folder, “is laying it on pretty thick. And a lot of your profile is not even me.” She slams the folder on the table while craning her neck to undo some of her tension. “Explain.”

“Sherlock Holmes can detect a lie even if you don’t open your mouth. The cover has to be as close to the truth.” Natasha starts. “I can be discreet but you; anyone can read you with one look and dismiss you immediately. “

Molly shoots her an indignant glare and was about to run her mouth off to protest.

Natasha cuts her off before she does. “Let me finish…”

Molly backs down and falls on the stool again.

“Which is why I recommended you. SHIELD knows you’re brilliant or at least anyone who’s worked with you knows. But if you recall, people used to look over you because you have a presence of a mouse. We don’t need stealth, we need invisibility.”

Molly still rolls her eyes. “You basically insulted and complimented me right there. I know that and I’ve used it on previous missions too. But this cover, which by the way is not a cover, will open doors that I have locked and have thrown away the keys to. And at the possibility of a blown cover, I will have to change my name so as not to turn up in MI-5’s list of persons of interest. His brother is the British Government. There’s nothing in the SHIELD handbook about that!”

“Alright Doctor Goody-Two-Shoes, me and Clint will devise the exit strategy if it comes to that point. Don’t sweat the small stuff. This will be cake.” Natasha easily brushes off Molly’s overreaction.

“I don’t have a choice, do I?” Molly’s shoulders droop in defeat.

“If it were up to me, maybe… But it’s from the man upstairs.” Natasha covers her left eye with her left hand to simulate the eye patch.

Molly stifled a giggle, trying not to laugh at it. “Pffft! You’re a shitty friend, you know that? Hahaha!” She unsuccessfully stops herself from letting out a guffaw. Her laughter rings out in the lab, finally just letting her apprehensions go.

Natasha smiles and pats her back as the cackling doctor chokes a bit from her uncontrolled laughter.

“I’ll use that next time I reference the Director to Agent Hand. I might get an actual laugh from her.” Molly goes down to giggling as she calms herself from her outburst.

“Oh, I need proof when you catch her doing it. I don’t think I’ve even seen that woman smile before.” Natasha stands from the stool to take her leave. “We’ll start tomorrow. I suggest you find those keys you threw away. You’ll be taking them back to London with you.”  


	3. Chapter 3

“Specialist Registrar”

Molly Hooper reads out the title in her St. Bartholomew’s ID card. She didn’t even take the 8 years training for her to get a specialty because she was plucked out of medical school after graduation but luckily her SHIELD career had advanced her knowledge in both forensics and medicine. She leaned towards forensics but she was also an active medical officer. But now according to Natasha, this version of Molly Hooper is a pathologist. Dead bodies and crime scenes; which isn’t a bother but maybe a little step backwards from her usual fair of unusual cases. SHIELD has her studying people with extraordinary abilities, organic biological anomalies, and the like.

St. Bartholomew’s Hospital is a teaching hospital and occasionally deals with the NSY. Mostly her job would be getting cause of death and telling families how their loved ones died or doing lab work from crime scenes.

“Oh well, there may be a serial killer or two to spice things up, I suppose.” She thinks out loud. 

It’s her first day in her new cover job. She stands in the middle of her small kitchen. The flat they found is a charming two-bedroom with ample space for one person. She and Natasha had decorated the place two days ago to fit her “personality”. It had a horrible color scheme but it gave the place a eclectic vibe just like how Natasha describes this Molly Hooper.  Her personal wardrobe, which wasn’t much, had to evolve as well. Natasha got her clothes that were unflattering to her figure and had a childish quality. And fruits. There were several pieces with strawberries and cherries.

“You have to look like the least threatening person in the world.” Natasha defended her choices.

“Yah. But I’m already invisible. How could this,” she held up the cardigan with cherries all over, “make me unseen. It’s like a target on my back. I’d be made fun of like in 6th form when my dad made me where an ugly jumper for picture day that my nana made for me.”

“Because it doesn’t scream SPY when you wear it. Pathologist Molly Hooper is this kind of person. I even got you this furball,” She picked up the orange tabby kitten by her feet and held him by his two front paws. “Toby here is gonna make you look like the cat lady you might have been if you weren’t recruited by SHIELD.”

Molly glared. “That’s offensive, you know…  I was a child prodigy. If I wasn’t with SHIELD I’d probably had dozens of offers from the top medical research facilities all over the world. I’d probably be a celebrated name in my chosen field too.”

“Sure, if you grew out your pushover-ness . You’ve let people take credit for your work before. Your SHIELD training took some of that out of you. But then you’re still kind of a pushover…” Natasha plumped down the couch with Toby still in her arms.

Molly considered it, and she was probably right. She would’ve been pushed to the background while others took advantage of her kind nature. She’s gotten a little more edge from the self-defense training and field work experience. But underneath, she is still that bullied little girl who was too strange to fit in anywhere.

That conversation happened yesterday and today is the first day of Specialist Registrar, Molly Hooper. Natasha will be shadowing her in a few days as a lab technician so today Molly’s new self will be put to the test. She‘s wearing a striped blouse underneath a bright teal jumper and loose khaki slacks and some low heeled pumps. She refuses to wear the cherry cardigan and saves it for another day. She leaves her flat at seven thirty in the morning to take the tube and hopefully arrive at Barts by eight AM.

London hadn’t changed that much since she left eight years ago. It’s as dreary and busy and she feels this as she journeys her way to work. She takes her earphones from her bag and listens to a bit of classic 80s music to calm herself down. The anxiety she’s feeling is showing in her fingers so she grips the pole nearest to her as tightly as she could.

Natasha tried to assure her yesterday that Sherlock Holmes might not show up because of his sporadic and impulsive behavior so she just needs to take the cover as seriously as she takes her real job.  Everything will follow after that.

She arrives at Barts with two minutes to spare. She rushes to the lifts as one was about to close and she asks the operator where the morgue was. The lady presses the basement floor and then the close button. When she gets to her floor, she beelines to the reception area.

“Excuse me, where can I find Dr. Stamford?” Molly asks the reception lady. The lady points to the left and says, “At the end of the hall.”

Molly thanks her and rushes through the wide lit hall.

She pushes the glass door with the name Dr. Michael Stamford, SpR and finds a plump middle-aged man who looks startled at her entrance.

She winces a bit as she forgets to knock in her haste. “Sorry. Dr. Stamford?”  She closes the door behind her and settles to stand near it.

“Yes?” Mike Stamford, the head of the pathology department, looks at her with some confusion. His eyebrows rise as he realizes that she was the newly hired pathologist. “Oh, you’re Dr. Hooper, I presume.” He stands to shake her hand and guides her to take a seat.

“Sorry to barge in… I thought I was late.” She gestures to the time on the wall clock that read ten minutes after eight.

Dr. Stamford smiles at her to ease her worry about the time. “Oh, it’s not a problem. I’m not that strict with schedules. I just got here myself a few minutes ago.” His hands shuffle through his inbox on his desk, looking for her CV. “I’m so relieved that you could come at short notice. The department’s not that big, you see. We have a handful of assistants that leave as quickly as they come. So when one of our pathologists quits on you due to… um…” He tries to find the words to describe the circumstances of the person she’s taking over for. “Difference in opinions, to say the least, your immediacy to come here is very much obliged.” He smiles again and finally holds the CV in his hands.  He scans the document for a bit and Molly grips her handbag a little tighter knowing some of the information in there were lies.

“Wow, you graduated so young. And well published too.” He flips through the pages. Molly tries to remember the details she and Natasha had put in there. The cover was tight because those articles she wrote were published under her real name. But how she got her specialty, that’s where the lies came in.

“Edinburgh, and you’re only 30, right?”

“Yes. I just finished my training a few months back.” Molly exhales after holding her breath from nervousness. Her confidence in her cover is slowly dropping by the minute. If she couldn’t get her nerves in check, she doesn’t know how she could ever pull this off.  

Dr. Stamford could sense her tension. He chalks it off to this being her first day and all. He suddenly remembers the cause of the other pathologist leaving and looks at the fidgeting girl in front of him. ‘He would eat her alive…’ He silently worries that the problem might drive this exceptional doctor from his staff as soon as they meet. He decides that a warning might prepare her for Sherlock Holmes.

“Excellent…” He hesitates but presses on. “Uh… I do have to warn you though. We work with Scotland Yard from time to time and they usually bring this consultant with them.”

Dr. Stamford’s uncomfortable smile could only mean that he was talking about her target. “Consultant? Like another doctor?”

“Oh no. Not a doctor… although he has a degree in Chem.” He mumbles that last part. “He’s a detective… but he’s not part of the NSY. They have him look at the bodies and he deduces how they died. It’s impressive really. He could spew details about a person just by looking at the dirt in their shoes.”

“Okay, but what’s wrong with him then?”

Before Dr. Stamford could answer, a tall figure with dark curly hair, a blue scarf, and a long black trench coat barges in. “Mike, I need to see a body that came in early this morning. Your terrible staff is preventing me from seeing it.”

“Is the DI with you? Or are you here by yourself?” Mike stands to lead the intruder out of his office. He doesn’t want Sherlock Holmes to drive away his new hire before she could start.

“I see you’ve replaced that imbecile.” Sherlock sets his eyes on Molly and she twists her body to face the detective.  She could already sense he was deducing her.

“Yes, I have. C’mon, I’ll help you out with Dr. Fuller.” Mike pushes Sherlock to the door before he does some damage. He has the detective outside his office before popping his head back in, “I’ll be back in a while. Make yourself comfortable.”

And with that, she’s left to ponder that brief exchange.

**Notes for the Chapter:**

> I down played their first meet since I’m not that credible with romance. The crush would be a gradual thing and not immediate. I’m not going for romance anyway but there has to be a small element of it since it’s in canon. And I think it’s natural for her to grow feelings for him whether if it was for the sake of the cover or not. 
> 
> I'd love some feedback. Leave a comment, if you can. :D


	4. Chapter 4

The first time she saw Sherlock Holmes, he didn’t really leave a remarkable impression. There was a glance and then he was gone. The second time was a few weeks later while she was working on several bodies that died in a fire. Natasha had started shadowing her a week ago and the spy was a few meters away when the consulting detective burst in the morgue doors with a silver-haired man on his tail.

“Don’t be daft Sherlock! We still don’t have evidence it was arson!”

“I assure you, Detective Inspector, that fire was not an accident. There’s just too much damage to sift through, but rest assured that it was a work of an arsonist.” Sherlock had finally turned his head to see that he would be working with the new pathologist. He immediately raised a brow and protested.

“Where’s Dr. Stamford? He should have told you that I don’t work with anyone else other than him.”

Molly frowned. This man had some nerve to immediately dismiss her without even giving her a chance. She already looked at the bodies an hour ago. She hasn’t started the post-mortem but one of them had already stood out. There were 12 bodies all in all; 6 male adults, 4 females, and 2 children. One female body was too charred to be recognized and she must have been in the one closest to the source. According to the initial inquiries, one of the males was the super of the building. He suffered 3rd degree burns and died of asphyxiation from the fumes as most of them did. The unrecognizable woman however, had hidden multiple gunshot wounds from her initial inspection. It was hard to see it if you didn’t have an eye for it. But Molly had immediately flagged it once she had seen the body. She and Natasha had bounced ideas off each other before the consulting detective had intruded.

“Dr. Stamford is at a conference in Switzerland. I’ve just started my initial examinations.” Molly started confidently.

Natasha eyed her from her place but didn’t speak up to stop her from running her mouth.

Sherlock grimaced and glared at her. His face was showing great displeasure from the notion of working with someone who looked like she could be blown by the wind. He remembered her from a few weeks ago when he barged in her interview. Her form was shaking like a leaf and her small stature and round doe eyes made her look more like a baby cow trying to stand and falling. Even as she stood in front of him with her firm and professional voice, all he saw a little girl trying to be a grown up and looking a little too green.

“Sorry Doctor, don’t mind him.” The DI took over and stepped in front of Sherlock. “What did you find from the bodies?”

Molly inhaled and licked her lips and walked to the start of the lined examination tables.  Sherlock’s glare followed her, waiting for her to make a mistake so he could chew her out for it.

She started to point out the details for each body; not missing a beat and the consulting detective looked unimpressed. She reached the final two bodies, the super and the charred woman, and started to point out the differences from the others.

“This is Mr. Henry, the super of the building. 50-year-old male, 169cm, suffered third degree burns and some pre-mortem bruising in his abdomen. Cause of death is asphyxiation through smoke inhalation. I also found a wound in between his index finger and thumb in the right hand. I took some samples from it to test for gunshot residue…”

“And why would you do that Doctor…” Sherlock cuts her off.

“Hooper.” She raises her id badge and proceeds to explain. “Because,” She moves to the next body of the charred woman. “She had multiple gunshot wounds, here” pointing to the shoulder, “here,” pointing to the chest, “and here,” pointing to the abdomen.

Sherlock and the DI moved closer to inspect the body. It was hard to see the bullet wounds since the body was fully burnt but after the closer look, they saw the small penetration wounds that were almost closed off by burnt flesh.

Sherlock just raised a brow. He was slightly annoyed that he couldn’t find fault to her work but covered by not acknowledging it.

“Lestrade, I need to see the crime scene now that the fire is out. But this is obviously arson to cover up for murder… Barely a 4.,.” He trailed off and adjusted his Belstaff coat and barged out like he had come in.

The DI, now that she knew his name was Lestrade, smiled sheepishly and looked apologetic. “Thank you Doctor Hooper.” He shook her hand. “I didn’t know Mike had already replaced Dr. Jordan. He didn’t get along with Sherlock so... you know. You’re very astute for someone so young.”  He complimented how she was able to make the arrogant detective shut up.

“I hope you stay on.” It was better than saying good luck. But then he felt, she might need it if she does stay on.

He took his leave and with only the two of them left in the lab, Natasha finally spoke up. “Was that a character choice, Hooper? Or did you compromise your cover already?

Molly glared and huffed. “Excuse you, NATALIE. But if I am to stay here in London indefinitely, I can’t be seen as incompetent. I graduated top marks so just piss off…” Molly reeled in her annoyance at her “C.O.”.

“Okay, but if you’re going to insist on having some backbone, you better make damn sure he won’t sniff a clue about you. If he starts getting curious, he’s going to pick you apart. The beauty of being a mouse is that you don’t get noticed.” Natasha bit back.

“Yes. I know. And it’s working.” Molly stood her ground and haughtily crossed her arms. “You just don’t see it yet.” She sent a fake smile and proceeded to the storage room to get her equipment for the autopsies.

“We’ll see.” Natasha sent her a bemused look.

Molly came out of the room and tossed her an operation gown. Natasha caught it and gave her a confused look.

Molly smiled evilly at her. “You’re helping me with postmortems.”

**Notes for the Chapter:**

> I'll apologize for the tense shifting. It's my worst habit as a writer. I just forget most of the time or my brain doesn't register it until I've written oodles of words. 
> 
> I will move the story faster but I think it's important that I flesh out some details before heading into the canon stuff. 
> 
> I still have no feedback. :( I want to know what you guys think of it. I'd post it in FF.net but I'm still trying to figure out under which category should I put it since there is no MCU there.


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